Confession: I used to love the giant poppyseed muffins from Costco as a kid. But that was then, and this is now—where we know better, and make all the things with better-for-you ingredients. Like these Healthy Lemon Poppyseed Protein Muffins. Soft, fluffy, and drizzled with the dreamiest lemon glaze, these are a must. They’re gluten-free, dairy-free, and taste like heaven. Prepare to be obsessed!
Bright, Protein-Packed Lemon Poppy Seed Muffins
Another confession: I’m a sucker for anything lemon poppyseed (as evidenced by another recent recipe I shared—Lemon Poppyseed High-Protein Pancakes, also GF and DF). It’s the most underrated muffin flavor, if you ask me.
Especially in the spring, there’s just something about that lemon poppyseed taste that always hits. Fresh, zesty, and comforting all at once.
I’ve been so excited to share these healthy lemon poppyseed muffins because they’re perfectly sweet and full of that citrusy flavor we love, but protein-packed and made with nourishing, feel-good ingredients like almond flour, eggs, and raw honey.
I love making a batch of these cuties at the start of the week for a quick meal prep breakfast, post-workout snack, or a healthy treat with my afternoon matcha.
Made with Clean Ingredients You Can Feel Good About
Ok, last confession I’ll make is that I’ve legit dreamt of these perfect little lemon poppyseed protein muffins. High in protein, naturally sweetened, and completely gluten-free and dairy-free, they’re unreal, you guys!
Each muffin is powered by wholesome, real-food ingredients. Almond flour and pasture-raised eggs give these muffins a boost of healthy fats and protein—along with the vanilla protein powder which really amps up the protein content and overall flavor—while the poppyseeds add fiber and a little crunch.
Fresh lemon juice and zest brighten the flavor naturally, and the creamy lemon glaze made with coconut butter takes them to the next level.
These muffins are not only gluten- and dairy-free, but also refined sugar-free, and a great option if you’re following a paleo-friendly or clean eating lifestyle.
A Healthy Muffin You’ll Want to Make on Repeat
So, if you’re thinking about making this easy, high-protein muffin recipe, then what are you waiting for?! Get on it!
Spring is here and it’s the perfect time to whip these up, and use any extra lemons you have laying around in your kitchen.
Simple to make, freezer-friendly, and family-approved—this one checks all the boxes. Top them with extra lemon zest for a little something special—and don’t forget to tag me @rachaelsgoodeats if you bake a batch. I love seeing what you’re making in your kitchens. Enjoy!
INGREDIENTS YOU’LL NEED:
For the protein muffins:
- Almond flour
- Vanilla protein powder (I used Ritual)
- Poppy seeds
- Baking powder
- Sea salt
- Pasture-raised eggs
- Unsweetened almond milk
- Fresh lemon juice
- Lemon zest
- Raw honey or pure maple syrup
- Vanilla extract
- Melted coconut oil
For the lemon glaze:
- Fresh lemon juice
- Melted coconut butter (for a creamy, dairy-free glaze)
- Pure maple syrup or raw honey (adjust for sweetness)
- Zest of 1 lemon for garnish (optional)
HOW TO MAKE HEALTHY LEMON POPPYSEED PROTEIN MUFFINS (GLUTEN-FREE + DAIRY-FREE)
To make the protein muffins:
Line a muffin tin with 12 liners.
In a large bowl, whisk together the dry ingredients: almond flour, protein powder, poppy seeds, baking powder, and sea salt.
In a separate bowl, whisk together the wet ingredients: eggs, almond milk, lemon juice, lemon zest, honey, vanilla extract, and melted coconut oil.
Pour the wet ingredients into the dry ingredients, and stir until just combined. Divide the batter evenly between muffin liners.
Bake for 18-20 minutes, or until a toothpick inserted in the center comes out clean. Let muffins cool completely.
To prepare the lemon glaze:
In a small bowl, whisk together the lemon juice, melted coconut butter, and honey (or maple syrup) until smooth and pourable. If too thick, add a little more lemon juice.
To glaze the muffins:
Once muffins are cool, drizzle the glaze over each muffin.
Sprinkle with additional lemon zest if desired. Allow the glaze to set for about 5 minutes. Serve and enjoy!
How to store:
Store muffins in an airtight container at room temp for 1–2 days or in the fridge for up to 5 days. For longer storage, freeze (unglazed) for up to 2 months—just thaw overnight or warm them up before enjoying.
RECIPE SUBSTITUTIONS & QUESTIONS
Swap maple syrup and honey interchangeably based on your preference. If no dairy restrictions, regular milk works, or unsweetened cashew milk if you don’t have almond milk. You can also try avocado oil or olive oil instead of coconut oil.
No almond flour? A gluten-free flour blend can work, but texture may change slightly (may be more cake-like and less moist than almond flour), and measurements may need to be adjusted. Coconut flour is not a 1:1 swap and would require major adjustments, so it’s not recommended for this recipe.
If you don’t have poppy seeds, chia seeds are a great stand-in. And for the glaze, coconut butter can be replaced with cashew butter for a slightly different but still creamy finish. Let me know if you try any of these swaps; I’ve only made this recipe as-is 😊
As for protein powder brands, I love Ritual, but have a list of My 6 Favorite Protein Powders (click here), if you’re looking for recommendations.
Do I have to soak poppy seeds before baking?
Nope, soaking isn’t necessary for this recipe. The poppy seeds soften slightly as the muffins bake, so you’ll still get that signature texture without any extra prep. Just stir them right into the batter!
Can I make these muffins without protein powder?
Yes! You can leave out the protein powder if needed—just replace it with an extra ¼ cup of almond flour to maintain the right texture. Keep in mind the muffins will have slightly less protein but still be just as delicious and satisfying.
HEALTHY, HIGH-PROTEIN BREAKFAST RECIPES FOR BUSY MORNINGS:
Avo Chimichurri Breakfast Tacos
Chocolate Banana Blender Muffins (Gluten-Free)
High-Protein Chocolate Chunk Almond Butter Smoothie
Lemon Poppyseed High-Protein Pancakes (Gluten-Free, Dairy-Free)
Click here to watch the reel I made of this recipe 🙂
Healthy Lemon Poppyseed Protein Muffins (Gluten-Free + Dairy-Free)
Ingredients
For the protein muffins:
- 2 cups almond flour
- ½ cup vanilla protein powder, (I used Ritual)
- 4 tablespoons poppy seeds
- 2 teaspoons baking powder
- ½ teaspoon sea salt
- 4 pasture-raised eggs
- ½ cup unsweetened almond milk
- 4 tablespoons fresh lemon juice
- 2 tablespoons lemon zest
- 4 tablespoons raw honey or pure maple syrup
- 2 teaspoons vanilla extract
- 4 tablespoons melted coconut oil
For the lemon glaze:
- 2 tablespoons fresh lemon juice
- 2.5 tablespoons melted coconut butter, (for a creamy, dairy-free glaze)
- 1 tablespoon raw honey or pure maple syrup, (adjust for sweetness)
- Zest of 1 lemon for garnish, (optional)
Instructions
To make the protein muffins:
- Preheat the oven to 350°F (175°C).
- Line a muffin tin with 12 liners.
- In a large bowl, whisk together the dry ingredients: almond flour, protein powder, poppy seeds, baking powder, and sea salt.
- In a separate bowl, whisk together the wet ingredients: eggs, almond milk, lemon juice, lemon zest, honey, vanilla extract, and melted coconut oil.
- Pour the wet ingredients into the dry ingredients, and stir until just combined. Divide the batter evenly between muffin liners.
- Bake for 18-20 minutes, or until a toothpick inserted in the center comes out clean. Let muffins cool completely.
To prepare the lemon glaze:
- In a small bowl, whisk together the lemon juice, melted coconut butter, and honey (or maple syrup) until smooth and pourable. If too thick, add a little more lemon juice.
To glaze the muffins:
- Once muffins are cool, drizzle the glaze over each muffin.
- Sprinkle with additional lemon zest if desired. Allow the glaze to set for about 5 minutes. Serve and enjoy!
How to store:
- Store muffins in an airtight container at room temp for 1–2 days or in the fridge for up to 5 days. For longer storage, freeze (unglazed) for up to 2 months—just thaw overnight or warm them up before enjoying.
